Sentence examples for package pipeline from inspiring English sources

Samples with low bisulphite conversion (BS) efficiency (BS control intensity values < 4000) were immediately excluded from the analysis as well as samples that failed the quality control analysis performed according the IMA package pipeline.

In this work, we introduce a Perl-based software pipeline that integrates multiple free software packages to predict protein structures and structural properties [19].

Using the software package MaSuRCA pipeline, a K-mer length of 81 has been selected by jellyfish, included in the MaSuRCa pipeline, which was close to the k-mer length of 87 suggested by Kmergenie.

As an illustration of the widely differing methods currently being used, one of the above-referenced papers used Illumina sequencing data processed with the Short Oligonucleotide Analysis Package (SOAP) pipeline [ 2] whereas the other group used Illumina sequencing data processed with the Genome Analysis Toolkit (GATK) pipeline [ 1].

The package and pipeline for producing it are available from http://bcb.dfci.harvard.edu/ovariancancer.edu/ovariancancer

IB and AT designed and packaged the pipeline.

We would like to thank Lucilla Luzi for giving the idea of packaging this pipeline.

Several packages provide pipelines to bring these new algorithms into the lab [ 12, 13].

These data allow us to evaluate the different software packages and pipelines at different numbers of replicates covering a variety of practical research settings.

For a practical comparison of the software packages and pipelines in real data sets, we considered two publicly available data sets that were among the few with relatively large numbers of replicates.

To assess how the different software packages and pipelines can control false positive rates, we utilized the multiple replicates within the sample groups by constructing artificial two-group comparisons.